Technical Abstract:
Recent developments in sequencing technology have allowed the generation of millions of short read sequences in a fast and inexpensive way. This enables the cost effective large scale identification of hundreds of thousands of SNPs needed for the development of high density SNP arrays. Currently, a high density swine SNP chip is being developed as part of an integrated effort of several European and American institutions involved in swine genomics research. The future pig SNP chip will include already validated SNPs as well as SNPs identified de novo using second generation sequencing on the Illumina 1 G analyzer (Solexa) and the Roche 454 sequencer. Towards this end, a total of 15 DNA libraries were prepared using pooled DNA samples from five breeds (Duroc, Landrace, Large White, Pietrain and Wild Boar) digested with three restriction enzymes (AluI, HaeIII, MspI). Fragments in the size range of 150-200 bp were selected for sequencing. The ends of these fragments (35 bp) will be sequenced at 30X coverage complemented with 2X sequencing of the complete fragment using 454 sequence technology. The Solexa short sequence reads will be filtered using several quality criteria to produce the dataset used for SNP discovery. Additional criteria for the selection of the 60K SNPs include the estimated minor allele frequency and genome position of the SNPs. The high density 60K SNP chip will be an extremely valuable tool for the pig genomics community for a variety of applications including QTL and LD mapping, association studies and genomic selection.